Contacts of the helix formed by residues 453 - 464 (chain B) in PDB entry 2EIT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 453 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B THR* 3.3 19.5 + - + +
451B SER* 3.0 12.5 + - - +
452B ARG* 1.3 76.6 - - - +
454B ARG* 1.3 65.4 + - - +
455B GLU* 3.2 32.3 + - - +
456B HIS* 3.0 56.1 + - + +
457B LEU* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLU* 2.8 43.0 + - - -
516A PHE* 4.6 7.2 - - - -
452B ARG* 3.3 12.3 + - - +
453B LYS* 1.3 70.8 - - - +
455B GLU* 1.3 68.2 + - - +
457B LEU* 3.3 21.0 + - - +
458B GLU* 2.8 56.8 + - + +
472B ASN* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LYS* 3.2 37.2 + - - +
454B ARG* 1.3 82.9 + - + +
456B HIS* 1.3 61.0 + - + +
458B GLU* 4.5 3.8 - - - +
459B TRP* 3.0 30.5 + - - +
462B ARG* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ASP* 2.7 26.9 + - + -
300B THR* 5.5 2.0 - - + -
431B PHE* 3.4 59.0 - + + +
451B SER* 3.8 9.0 - - - +
453B LYS* 3.0 44.7 + - + +
455B GLU* 1.3 78.9 - - + +
457B LEU* 1.3 67.0 + - - +
459B TRP* 3.3 10.6 + + - -
460B ALA* 3.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLU* 3.7 15.0 - - - +
449B VAL* 3.9 25.8 - - + +
451B SER* 3.9 26.0 - - - +
452B ARG* 5.1 1.6 - - - -
453B LYS 3.1 17.4 + - - +
454B ARG* 3.5 37.9 - - - +
456B HIS* 1.3 75.7 - - - +
458B GLU* 1.3 62.2 + - + +
460B ALA* 3.1 3.4 + - - -
461B ARG 2.9 23.2 + - - -
471B PHE* 3.1 45.1 - - + -
472B ASN* 4.1 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLU* 4.8 0.3 - - - +
454B ARG* 2.8 48.2 + - + +
455B GLU* 4.5 3.8 - - - +
457B LEU* 1.3 75.3 - - + +
459B TRP* 1.3 61.2 + - - +
461B ARG* 2.9 43.4 + - - +
462B ARG* 3.3 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PHE* 3.6 28.0 - + + -
432B ALA* 3.5 34.3 - - + -
435B LEU* 3.7 19.3 - - + +
455B GLU 3.0 22.4 + - - +
456B HIS* 3.5 15.7 - + - +
458B GLU* 1.3 77.2 - - - +
460B ALA* 1.3 56.5 + - - +
462B ARG* 3.2 31.1 + - - +
463B GLU* 2.8 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A LYS* 3.4 0.5 + - - -
431B PHE* 4.2 1.5 - - + -
435B LEU* 4.2 12.1 - - + -
449B VAL* 3.8 28.9 - - + -
456B HIS 3.0 12.5 + - - +
457B LEU* 3.1 8.5 + - - +
459B TRP* 1.3 73.4 - - - +
461B ARG* 1.3 66.7 + - - +
464B PHE* 2.9 40.4 + - + +
469B LEU* 3.3 6.1 - - - +
471B PHE* 3.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 3.9 11.2 - - + -
166A ASP* 4.5 10.2 + - - -
168A GLU* 2.9 40.1 + - - +
170A PHE* 3.7 24.1 - - + -
510A LYS* 2.8 20.8 + - - +
512A VAL* 3.4 33.3 + - + +
514A GLU* 4.4 16.0 + - - +
457B LEU 2.9 12.6 + - - +
458B GLU* 2.9 40.4 + - - +
459B TRP 3.3 0.2 - - - -
460B ALA* 1.3 75.3 - - - +
462B ARG* 1.3 60.3 + - + +
469B LEU* 4.0 10.8 - - - -
471B PHE* 3.7 24.0 - - + -
2520B ACT 3.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 4.5 3.9 + - - +
92A ASP* 5.4 7.3 + - - +
170A PHE* 5.7 0.7 - - - -
455B GLU 5.4 0.2 + - - -
458B GLU* 3.3 17.4 + - + +
459B TRP* 3.2 34.5 + - - +
460B ALA 3.0 0.2 - - - -
461B ARG* 1.3 84.8 - - + +
463B GLU* 1.3 86.8 + - + +
464B PHE 4.0 0.2 - - - -
2520B ACT 3.3 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 3.1 30.0 + - - -
92A ASP* 4.4 6.2 - - - +
435B LEU* 4.7 7.9 - - + -
439B ASN* 2.9 24.7 + - - +
459B TRP* 2.8 38.1 + - + +
462B ARG* 1.3 104.8 + - + +
464B PHE* 1.3 59.5 + - - +
465B HIS* 3.2 6.2 + - - +
2520B ACT 4.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A LYS* 2.7 27.1 + - - -
294B ALA* 3.7 13.7 - - + -
296B ILE* 3.6 20.6 - - + -
327B ARG* 5.5 0.7 - - - -
435B LEU* 3.7 14.8 - - + +
438B ALA* 3.7 27.8 - - + -
439B ASN* 3.9 5.4 - - - -
446B THR 4.9 0.4 - - - -
447B GLY* 3.7 16.2 - - - -
448B GLY 3.5 26.2 - - - -
449B VAL* 3.8 13.2 - - + -
460B ALA* 2.9 19.8 + - + +
463B GLU* 1.3 73.2 - - - +
465B HIS* 1.3 57.9 + - - +
466B VAL* 2.9 36.0 + - + +
469B LEU* 3.6 16.4 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il